Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MITF

Cell type

Cell type Class
Muscle
Cell type
SU-CCS-1
Tissue
Soft Tissue
Cell Type
Clear Cell Sarcoma Cell Line
Disease
Clear Cell Sarcoma

Attributes by original data submitter

Sample

source_name
Cell line
cell type
Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor
chip antibody
MITF (#91201, Active motif)
treatment
Transfected with CTRL siRNA
cell line
SU-CCS-1 ATCC CRL-2971

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with formaldehyde, flash-frozen and processed for ChIP using Protein G beads. ChIP DNA was purified with AMPure XP beads. ChIP DNA libraries were prepared using the Illumina TruSeq ChIP library preparation kit (Illumina cat. no. IP-202-1012 or IP-202-1024) according to the manufacturer's instructions and 200-500 bp fragments selected using AMPureXP beads.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
29312804
Reads aligned (%)
98.3
Duplicates removed (%)
16.8
Number of peaks
80499 (qval < 1E-05)

hg19

Number of total reads
29312804
Reads aligned (%)
97.8
Duplicates removed (%)
17.3
Number of peaks
80101 (qval < 1E-05)

Base call quality data from DBCLS SRA